Merge branch 'release-0.2.1'

Conflicts:
	site/app/docs/js/coffee/docs.coffee
	site/app/views/nav.html

Author: huston

BUILD.md

@@ -66,7 +66,7 @@ bower install
 
 # Install Jekyll and its depedencies
 gem install jekyll 
-gem install codearray
+gem install coderay
 gem install kramdown
 
 # Run the documentation locally

Gruntfile.coffee

@@ -9,19 +9,19 @@ module.exports = (grunt) ->
   require("load-grunt-tasks") grunt
   require("time-grunt") grunt
   pkg = grunt.file.readJSON('./package.json')
-  
+
   if grunt.file.isFile('./s3.yml')
     s3Config = grunt.file.readYAML('./s3.yml')
     key_id = s3Config.AWS_ACCESS_KEY_ID
     secret = s3Config.AWS_SECRET_ACCESS_KEY
   else
     key_id = ''
     secret = ''
-  
-  grunt.initConfig    
+
+  grunt.initConfig
     # Project settings
     yeoman:
-      
+
       # Configurable paths
       app: "app"
       dist: "dist"
@@ -93,13 +93,13 @@ module.exports = (grunt) ->
           livereload: "<%= connect.options.livereload %>"
 
         files: ["<%= yeoman.app %>/{,*/}*.html", ".tmp/styles/{,*/}*.css", ".tmp/scripts/{,*/}*.js", "<%= yeoman.app %>/images/{,*/}*.{gif,jpeg,jpg,png,svg,webp}"]
-    
+
     # The actual grunt server settings
     connect:
       options:
         port: 9000
         livereload: 35729
-        
+
         # Change this to '0.0.0.0' to access the server from outside
         hostname: "localhost"
 
@@ -119,7 +119,7 @@ module.exports = (grunt) ->
           base: "<%= yeoman.dist %>"
           livereload: false
 
-    
+
     # Empties folders to start fresh
     clean:
       dist:
@@ -130,7 +130,7 @@ module.exports = (grunt) ->
 
       server: ".tmp"
 
-    
+
     # Make sure code styles are up to par and there are no obvious mistakes
     jshint:
       options:
@@ -139,15 +139,15 @@ module.exports = (grunt) ->
 
       all: ["Gruntfile.coffee", "<%= yeoman.app %>/scripts/{,*/}*.js", "!<%= yeoman.app %>/scripts/vendor/*", "test/spec/{,*/}*.js"]
 
-    
+
     # Mocha testing framework configuration options
     mocha:
       all:
         options:
           run: true
           urls: ["http://<%= connect.test.options.hostname %>:<%= connect.test.options.port %>/index.html"]
 
-    
+
     # Compiles CoffeeScript to JavaScript
     coffee:
       dist:
@@ -179,7 +179,7 @@ module.exports = (grunt) ->
           ext: ".js"
         ]
 
-    
+
     # Compiles Sass to CSS and generates necessary files if requested
     compass:
       options:
@@ -204,7 +204,7 @@ module.exports = (grunt) ->
         options:
           debugInfo: true
 
-    
+
     # Add vendor prefixed styles
     autoprefixer:
       options:
@@ -218,21 +218,21 @@ module.exports = (grunt) ->
           dest: ".tmp/styles/"
         ]
 
-    
+
     # Automatically inject Bower components into the HTML file
     "bower-install":
       app:
         html: "<%= yeoman.app %>/index.html"
         ignorePath: "<%= yeoman.app %>/"
 
-    
+
     # Renames files for browser caching purposes
     rev:
       dist:
         files:
           src: ["<%= yeoman.dist %>/scripts/{,*/}*.js", "<%= yeoman.dist %>/styles/{,*/}*.css", "<%= yeoman.dist %>/images/{,*/}*.{gif,jpeg,jpg,png,webp}", "<%= yeoman.dist %>/styles/fonts/{,*/}*.*"]
 
-    
+
     # Reads HTML for usemin blocks to enable smart builds that automatically
     # concat, minify and revision files. Creates configurations in memory so
     # additional tasks can operate on them
@@ -242,7 +242,7 @@ module.exports = (grunt) ->
 
       html: "<%= yeoman.app %>/index.html"
 
-    
+
     # Performs rewrites based on rev and the useminPrepare configuration
     usemin:
       options:
@@ -251,7 +251,7 @@ module.exports = (grunt) ->
       html: ["<%= yeoman.dist %>/{,*/}*.html"]
       css: ["<%= yeoman.dist %>/styles/{,*/}*.css"]
 
-    
+
     # The following *-min tasks produce minified files in the dist folder
     imagemin:
       dist:
@@ -299,7 +299,7 @@ module.exports = (grunt) ->
           '<%= yeoman.dist %>/alchemy.min.css': '.tmp/concat/styles/alchemy.min.css'
           '<%= yeoman.dist %>/styles/vendor.css': '.tmp/concat/styles/vendor.css'
               ]
-      
+
     uglify:
       dist:
         files: [
@@ -312,7 +312,7 @@ module.exports = (grunt) ->
             src: '.tmp/concat/scripts/vendor.js'
           }
         ]
-      buildAlchemy: 
+      buildAlchemy:
         files: [
           {
             dest: '<%= yeoman.dist %>/alchemy.min.js'
@@ -339,14 +339,17 @@ module.exports = (grunt) ->
             dest: '<%= yeoman.dist %>/styles/alchemy.css'
             src: '.tmp/styles/alchemy.css'
           }
+          {
+            dest: '<%= yeoman.dist %>/styles/alchemy-white.css'
+            src: '.tmp/styles/alchemy-white.css'
+          }
         ]
-      s3: 
+      s3:
         files: [
             dest: '.tmp/s3/alchemy.min.js'
             src: ['<%= yeoman.dist %>/scripts/vendor.js'
                   '<%= yeoman.dist %>/alchemy.min.js']
-          , # I think this comma format is elegant - if anyone hates it
-            # feel free to comment
+          , 
             dest: '.tmp/s3/alchemy.js'
             src: ['<%= yeoman.dist %>/scripts/vendor.js'
                   '<%= yeoman.dist %>/alchemy.js']
@@ -385,6 +388,10 @@ module.exports = (grunt) ->
             dest: '<%= yeoman.dist %>/alchemy.css'
             src: '.tmp/styles/alchemy.css'
           }
+          {
+            dest: '<%= yeoman.dist %>/alchemy-white.css'
+            src: '.tmp/styles/alchemy-white.css'
+          }
         ]
 
     # Copies remaining files to places other tasks can use
@@ -480,15 +487,15 @@ module.exports = (grunt) ->
     else
       grunt.task.run ["connect:test", "mocha"]
 
-  grunt.registerTask 'build', ["clean:dist", "useminPrepare", 
+  grunt.registerTask 'build', ["clean:dist", "useminPrepare",
                                 "copy:coffee", "concurrent:buildAlchemy",
                                 "copy:fonts", "copy:images",
-                                "autoprefixer", "concat:buildAlchemy", 
-                                "concat:generated", "cssmin:buildAlchemy", 
+                                "autoprefixer", "concat:buildAlchemy",
+                                "concat:generated", "cssmin:buildAlchemy",
                                 "uglify:buildAlchemy"]
-  
+
   releaseFlag = grunt.option('release')
-                           
+
   grunt.registerTask "default",
     if releaseFlag
       ["test",

README.md

@@ -10,9 +10,9 @@ Alchemy.js was built so that developers could easily get up and running with Gra
 Additionally, because Alchemy.js is built with d3, the core application can easily be extended with any of the other features included in d3.
 
 ##Quick Start and Documentation
-Learn how to get up and running with Alchemy.js in the [docs](http://graphalchemist.github.io/Alchemy/documentation/) and check our examples in our [examples gallery](http://graphalchemist.github.io/Alchemy/#/examples).
+Learn how to get up and running with Alchemy.js in the [docs](http://graphalchemist.github.io/Alchemy/docs/) and check our examples in our [examples gallery](http://graphalchemist.github.io/Alchemy/#/examples).
 ##Contributing 
-Read about how to contribute in the [docs](http://graphalchemist.github.io/Alchemy/documentation/Contributing/).
+Read about how to contribute in the [docs](http://graphalchemist.github.io/Alchemy/docs/#Contributing).
 
 ##Licensing
 The source is licensed under the AGPLv3 license for open source and open data projects.  For commercial licensing, get in touch with the [GraphAlchemist](mailto:team@graphalchemist.com) team. 

app/scripts/alchemy/clustering/clustering.coffee

@@ -63,12 +63,12 @@ class alchemy.clustering
 alchemy.clusterControls =
     init: ()->
         changeClusterHTML = """
-                            <h4>Cluster By:</h4>
-                            <input class='form-control' id='cluster-key' placeholder="Cluster Key"></input>
+                            <input class='form-control form-inline' id='cluster-key' placeholder="Cluster Key"></input>
                             """
         d3.select("#clustering-container")
             .append("div")
             .attr("id", "cluster-key-container")
+            .attr('class', 'property form-inline form-group')
             .html(changeClusterHTML)
             .style("display", "none")
 
@@ -78,7 +78,13 @@ alchemy.clusterControls =
             display = element.style("display")
 
             element.style("display", (e)-> 
-                if display == "block" then "none" else "block"))
+                if display == "block" then "none" else "block")
+
+            if d3.select("#cluster-key-container").style("display") == "none"
+                d3.select("#cluster-arrow").attr("class", "fa fa-2x fa-caret-right")
+            else d3.select("#cluster-arrow").attr("class", "fa fa-2x fa-caret-down")
+
+            )
 
         d3.select("#cluster-key")
             .on "keydown", -> 

app/scripts/alchemy/core/controls.coffee

@@ -15,8 +15,8 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 alchemy.controlDash = 
-    init: () ->
-        if alchemy.conf.showControlDash is true 
+    init: ->
+        if @dashIsShown()
             divSelector = alchemy.conf.divSelector
             # add dashboard wrapper
             d3.select("#{divSelector}")
@@ -44,7 +44,7 @@ alchemy.controlDash =
             alchemy.controlDash.stats()
             alchemy.controlDash.clustering()
 
-    search: () ->
+    search: ->
         if alchemy.conf.search
             d3.select("#control-dash")
                     .append("div")
@@ -57,7 +57,7 @@ alchemy.controlDash =
                           """)
             alchemy.search.init()
 
-    zoomCtrl: () ->
+    zoomCtrl: ->
         if alchemy.conf.zoomControls 
             d3.select("#control-dash-wrapper")
                 .append("div")
@@ -67,19 +67,19 @@ alchemy.controlDash =
                         <button id='zoom-in'  class='btn btn-defualt btn-primary'><i class='fa fa-plus'></i></button>
                         <button id='zoom-out' class='btn btn-default btn-primary'><i class='fa fa-minus'></i></button>")
 
-            d3.select('#zoom-in').on("click", () -> alchemy.interactions.clickZoom 'in' )
-            d3.select('#zoom-out').on("click", () -> alchemy.interactions.clickZoom 'out' )
-            d3.select('#zoom-reset').on("click", () -> alchemy.interactions.clickZoom 'reset')
+            d3.select('#zoom-in').on("click", -> alchemy.interactions.clickZoom 'in' )
+            d3.select('#zoom-out').on("click", -> alchemy.interactions.clickZoom 'out' )
+            d3.select('#zoom-reset').on("click", -> alchemy.interactions.clickZoom 'reset')
 
-    filters: () ->
-        if alchemy.conf.showFilters
+    filters: ->
+        if alchemy.conf.nodeFilters or alchemy.conf.edgeFilters
             d3.select("#control-dash")
                 .append("div")
                 .attr("id", "filters")
             alchemy.filters.init()
 
-    stats: () ->
-        if alchemy.conf.showStats
+    stats: ->
+        if alchemy.conf.nodeStats or alchemy.conf.edgeStats
             stats_html = """
                     <div id = "stats-header" data-toggle="collapse" data-target="#stats #all-stats">
                     <h3>
@@ -106,15 +106,13 @@ alchemy.controlDash =
 
             alchemy.stats.init()
 
-    clustering: () ->
+    clustering: ->
         if alchemy.conf.clusterControl
             clusterControl_html = """
-                    <div id = "clustering-container">
-                        <div id = "cluster_control_header" data-toggle="collapse" data-target="#clustering #cluster-options">
-                             <h3>
-                                Clustering
-                            </h3>
-                            <span class = "fa fa-2x fa-caret-right"></span>
+                    <div id="clustering-container">
+                        <div id="cluster_control_header" data-toggle="collapse" data-target="#clustering #cluster-options">
+                             <h3>Clustering</h3>
+                            <span id="cluster-arrow" class="fa fa-2x fa-caret-right"></span>
                         </div>
                     </div>
                     """
@@ -125,3 +123,11 @@ alchemy.controlDash =
                 .select('#cluster_control_header')
 
             alchemy.clusterControls.init()
+
+    dashIsShown: ->
+        conf = alchemy.conf
+
+        conf.showEditor    || conf.captionToggle  || conf.toggleRootNodes ||
+        conf.removeElement || conf.clusterControl || conf.nodeStats       ||
+        conf.edgeStats     || conf.edgeFilters    || conf.nodeFilters     || 
+        conf.edgesToggle   || conf.nodesToggle    || conf.search

app/scripts/alchemy/core/filters.coffee

@@ -55,9 +55,7 @@ alchemy.filters =
     show: () ->
         filter_html = """
                     <div id = "filter-header" data-toggle="collapse" data-target="#filters form">
-                        <h3>
-                            Filters
-                        </h3>
+                        <h3>Filters</h3>
                         <span class = "fa fa-2x fa-caret-right"></span>
                     </div>
                         <form class="form-inline collapse">

app/scripts/alchemy/core/startGraph.coffee

@@ -81,7 +81,7 @@ alchemy.startGraph = (data) ->
         defs = d3.select("#{alchemy.conf.divSelector} svg").append("svg:defs")
 
     if conf.directedEdges
-        arrowSize = conf.edgeArrowSize
+        arrowSize = conf.edgeArrowSize + (conf.edgeWidth() * 2)
         marker = defs.append("svg:marker")
             .attr("id", "arrow")
             .attr("viewBox", "0 -#{arrowSize * 0.4} #{arrowSize} #{arrowSize}")
@@ -98,6 +98,4 @@ alchemy.startGraph = (data) ->
 
     if conf.showEditor
         editor = new alchemy.editor.Editor
-        editor.startEditor()
-        # editor.nodeEditorInit()
-        # editor.edgeEditorInit()
+        editor.startEditor()